Digitizing collections to trace parasite-host associations and predict the spread of vector-borne disease

Digitizing collections to trace parasite-host associations and predict the spread of vector-borne disease (TPT)

TPT-TCN
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Project Summary
Current Research
Project Websites
Publications
Citizen Science!

Project Summary

Arthropod parasites (specifically, insects and their relatives) are responsible for economically critical issues in human health, wildlife conservation, and livestock productivity. Because natural history collections are permanent repositories for past and present parasite specimens, these collections and their data can help address these significant societal challenges in human and animal health and safety. Natural history collections often contain specimens and ancillary materials that are completely unknown to the broader community, yet represent irreplaceable knowledge about organismal habitats, distributions, and parasite-host associations. Further, these collections yield information that can be used to model ecological processes and changes in species distributions, predict the future spread of human and animal disease, update taxonomy, and help identify under-represented parasite groups in urgent need of sampling and threatened parasite diversity in need of conservation. This project will provide digital records (i.e., specimen label data and images) of invaluable arthropod parasite collections to make research-ready baseline data accessible online, catalyzing new research and education initiatives. These newly digitized data will have immediate and long-lasting benefits for our understanding of organismal associations, biodiversity, and beyond.

The Terrestrial Parasite Tracker Thematic Collection Network (TPT-TCN) will digitize over one million arthropod specimens representing species that are significant parasites and disease vectors of vertebrates in the United States. This digitization effort will integrate millions of vertebrate host records with vector and disease monitoring data shared by state and federal agency collaborators, creating a novel foundation for integrative, long-term research. This project is a collaboration of taxonomists and curators from vertebrate and invertebrate collections, as well as epidemiologists, ecologists, data-scientists, and biodiversity informatics specialists. This reach is further extended by the 26 collaborating research collections and other initiatives. This project will empower ongoing citizen science and public awareness campaigns with the tools to understand distribution changes of arthropod vectors and associated diseases due to environmental change and global movement. Public education initiatives include partnering with natural history museums to educate the public about parasites via science-focused lectures, exhibits, summer youth programs, informal presentations, and developing new online educational resources for teachers in underserved communities. All specimen images generated by this project will be used for the development of a rapid identification tool for parasites which will be made accessible through the internet and smartphone apps and shared with iDigBio (idigbio.org). The TPT-TCN will also develop and implement undergraduate teaching modules focused on data held in natural history collections. These modules will be disseminated to academic institutions across the United States and made available online.

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Project Websites & Social Media

Terrestrial Parasite Tracker
The original project home page.

Terrestrial Parasite Tracker Portal
Data portal and newer project home page with links to assorted resources.

GloBI Parasite Tracker
This Terrestrial Parasite Tracker (TPT) status page shows the current state of integration between TPT affiliated collections and Global Biotic Interactions (GloBI) which provides open access to finding species interaction data (e.g., predator-prey, pollinator-plant, pathogen-host, parasite-host) by combining existing open datasets using open source software.

TPT Taxonomy Resource Hub
This repository is meant to facilitate access to taxonomic resources produced by the Terrestrial Parasite Tracker project. It includes taxonomic name lists, name cleaning scripts, and contact information.

GloBI How-To
An instructional information page to assist in navigating and using data in GloBI

Interaction Data Interpretation Workshop
A free, reusable and modifiable lesson plan on biological interaction data.

Digitization Progress Reports
A resource for generating digitization effort graphs (or other efforts).

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Citizen Science & Outreach Projects

Notes from Nature - Terrestrial Parasite Tracker Portal
Become a citizen scientist and help out with the project! We have many ongoing projects and are frequently adding more. Check it out!

Parasite Palooza
FMNH’s free Museum days in October where Museum visitors take a closer look at parasites and can volunteer to work on Notes from Nature projects. Parasite Palooza Facebook page.

Bird Lice educational exhibit
Exhibit at UNH allows users to learn about the bird parasites by matching a bird with the lice that use it as a host. UNH collection homepage.

YPM EVOLUTIONS (Evoking Learning and Understanding through Investigations of the Natural Science)
A Free after school youth program for highschool students that helps prepare students for college and careers in science through classes, museum jobs, research internships, and other events. YPM EVOLUTIONS homepage.

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Project Leadership

Project Sponsor: Purdue University (NSF Award 1901932)

Principal Investigators (PIs): Stephen Cameron (PI), Jennifer Zaspel (co-PI)

Project Collaborators

Digitizing Institutions

Academy of Natural Sciences Philadelphia

Jason Weckstein, Academy of Natural Sciences Philadelphia, (NSF Award #1901935)

Purdue University

Stephen Cameron, Purdue University, (NSF Award #1901932)
Jennifer Zaspel, co-PI, Milwaukee Public Museum

University of California-Santa Barbara

Katja Seltmann, University of California-Santa Barbara, (NSF Award #1901926)

Texas A&M AgriLife Research

Jessica Light, Texas A&M AgriLife Research, (NSF Award #1901916)
John Oswald, co-PI

Field Museum of Natural History

Petra Sierwald, Field Museum of Natural History, (NSF Award #1901857)
John Bates, co-PI, Field Museum of Natural History

University of Nebraska-Lincoln

Scott Gardner, University of Nebraska-Lincoln, (NSF Award #1901911)

University of Minnesota-Twin Cities

Robin Thomson, University of Minnesota-Twin Cities, (NSF Award #1901915)
Ralph Holzenthal, co-PI, University of Minnesota

University of Wisconsin-Madison

Daniel Young, University of Wisconsin-Madison, (NSF Award #1902070)

Board of Regents, NSHE, obo University of Nevada, Reno

Julia Allen, Board of Regents, NSHE, obo University of Nevada, Reno, (NSF Award #1902031)
Robert Guralnick, co-PI, University of Florida

University of Hawaii

Daniel Rubinoff, University of Hawaii, (NSF Award #1901931)

University of Utah

Sarah Bush, University of Utah, (NSF Award #1901923)

California Academy of Sciences

Michelle Trautwein, California Academy of Sciences, (NSF Award #1901917)

Michigan State University

Anthony Cognato, Michigan State University, (NSF Award #1901958)

Bernice P Bishop Museum

James Boone, Bernice P Bishop Museum, (NSF Award #1901928)
Neal Evenhuis, co-PI, Bernice P Bishop Museum

University of New Mexico

Joseph Cook, University of New Mexico, (NSF Award #1901920)
Mariel Campbell, co-PI, University of New Mexico

University of Michigan Ann Arbor

Barry OConnor, University of Michigan Ann Arbor,(NSF Award #1902113)
(*Erika Tucker transferred to B.M. Oconnor 10/2021)

Brigham Young University

Michael Whiting, Brigham Young University, (NSF Award #1902048)

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Protocols & Workflows

TPT has contributed many exemplar workflows to the BugFlow repository as well as helped build many of the baseline workflow protocols on BugFlow. Specific exemplar workflows contributed include:

• Workflows folder (master/all workflows)
• Module 1A: Inventory and Taxonomy Update
• Module 3A: Direct Label Transcription
• Module 3C: Label data parsing
• Module 3D: Label Imaging
• Module 4C: Enveloped or "flat" Imaging
• Module 4F: Slide Label/low-res Imaging
• Module 4K: Pinned 2D non-stacked specimen imaging
• Module 4L: Vial low-res imaging

Imaging with the Terrestrial Parasite Tracker TCN Vimeo

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Publications

2022

• Poelen, Jorrit (2022). On Interpreting Biotic Association Records. Zenodo. https://doi.org/10.5281/zenodo.6686306

• Poelen, Jorrit H., Seltmann, Katja C., Campbell, Mariel, Orlofske, Sarah A., Light, Jessica E., Tucker, Erika M., Demboski, John R, McElrath, Tommy, Grinter, Christopher C, Diaz-Bastin, Rachel, Bush, Sarah E, Delapena, Robin, Cook, Joseph, Gall, Lawrence F., Whiting, Michael F, Clark, Shawn M, Cameron, Stephen L, Replogle, Charla R, Rund, Samuel S.C., Young, Daniel, Brabant, Craig, Sullivan, Kathryn, Turcatel, Maureen, Shuman Baquiran, Rebekah, Albion, Zoe, Austin, Kyhl, Rubinoff, Dan, Cognato, Anthony I., Caywood, Alyssa, Colby, Julia, Allen, Julie, Zaspel, Jennifer M. (2022). Terrestrial Parasite Tracker indexed biotic interactions and review summary (0.6) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6761707

• Tucker, Erika, Poelen, Jorrit, & Seltmann, Katja (2022). A lesson plan for better understanding entomological specimen interaction data in collections by NSF funded Terrestrial Parasite Tracker Thematic Collection Network [website: https://www.globalbioticinteractions/ecm-workshop/]. Zenodo. https://doi.org/10.5281/zenodo.6704580

• Dr. Nicolas J. Dowdy, Dr. Erika M. Tucker, Jorrit Poelen, Dr. Vijay Barve, Teresa Mayfield-Meyer, Kathryn Sullivan, & Dr. Jennifer M. Zaspel. (2022). njdowdy/tpt-taxonomy: TPT Taxonomic Resource v2.0.0 (v2.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7215550

2021

• Seltmann, Katja and Poelen, Jorrit and Sullivan, Kathryn and Zaspel, Jennifer. (2020). Making Parasite-Host Associations Visible using Global Biotic Interactions. Biodiversity Information Science and Standards 4: e58985. https://doi.org/10.3897/biss.4.58985

• Dowdy, N.J., Barve, V., Mayfield-Meyer, T., Sullivan, K., & Zaspel, J.M. (2021). njdowdy/tpt-taxonomy: TPT Taxonomic Resource v1.0.3 (v1.0.3) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5562742

• Poelen, Jorrit H., Seltmann, Katja C., Campbell, Mariel, Orlofske, Sarah A., Light, Jessica E., & Tucker, Erika M. (2021). Terrestrial Parasite Tracker indexed biotic interactions and review summary (0.5) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5572874

2020

• Cook, Joseph A and Arai, Satoru and Armién, Blas and Bates, John and Bonilla, Carlos A and Cortez, Maria Beatriz and Dunnum, Jonathan L and Ferguson, Adam W and Johnson, Karl M and Khan, Faisal Ali and Paul, Deborah L and Reeder, DeeAnn M and Revelez, Marcia A and Simmons, Nancy B and Thiers, Barbara M and Thompson, Cody W and Upham, Nathan S and Vanhove, Maarten P and Webala, Paul W and Weksler, Marcelo and Yanagihara, Richard and Soltis, Pamela S. (2020). Integrating Biodiversity Infrastructure into Pathogen Discovery and Mitigation of Emerging Infectious Diseases. BioScience. 70 (7) 531 to 534. doi:10.1093/biosci/biaa064

• Zaspel, Jennifer M and Allen, Julie M and Tyrrell, Christopher D and Lemoine, Nate and Jacobus, Luke M and Klem, Crystal and Goodwin, Jillian and Bates, John M. (2020). Human Health, Interagency Coordination, and the Need for Biodiversity Data. BioScience. 70 (7) 527 to 527. doi:10.1093/biosci/biaa065

• Poelen, Jorrit H., Seltmann, Katja C., & Campbell, Mariel. (2020). Terrestrial Parasite Tracker indexed biotic interactions and review summary (Version 0.2) [Data set]. doi: 10.5281/zenodo.3778773

• Poelen, Jorrit H., Seltmann, Katja C., Campbell, Mariel, Orlofske, Sarah A., & Tucker, Erika M. (2020). Terrestrial Parasite Tracker indexed biotic interactions and review summary (Version 0.1) [Data set]. doi: 10.5281/zenodo.3685365.

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Professional Presentations & Symposia

2022

• TPT Report Out. iDigBio sponsored. Virtual event page. Representatives from all 24 TPT primary data providers, as well as representatives from GloBI, SCAN, and Notes from Nature, gave presentations and project updates at the TPT Report Out. Event recording.

• Light, Jessica. Terrestrial Parasite Tracker: Digitizing collections to trace parasite-host associations and predict spread of vector-borne disease. 4th International Congress on Parasites of Wildlife. Kruger National Park, South Africa.

PENs

2020 Addition of the Yale Peabody Museum to the Terrestrial Parasite Tracker (TPT) Network

Arthropod parasites (specifically, insects and their relatives) are responsible for economically critical issues in human health, wildlife conservation, and livestock productivity. Because natural history collections are permanent repositories for past and present parasite specimens, these collections and their data can help address these significant societal challenges in human and animal health and safety. Natural history collections often contain specimens and ancillary materials that are completely unknown to the broader community, yet represent irreplaceable knowledge about organismal habitats, distributions, and parasite-host associations. Further, these collections yield information that can be used to model ecological processes and changes in species distributions, predict the future spread of human and animal disease, update taxonomy, and help identify under-represented parasite groups in urgent need of sampling and threatened parasite diversity in need of conservation. This project will provide digital records (i.e., specimen label data and images) of invaluable arthropod parasite collections to make research-ready baseline data accessible online, catalyzing new research and education initiatives. These newly digitized data will have immediate and long-lasting benefits for our understanding of organismal associations, biodiversity, and beyond.

The Terrestrial Parasite Tracker Thematic Collection Network (TPT-TCN) will digitize over one million arthropod specimens representing species that are significant parasites and disease vectors of vertebrates in the United States. The TPT-TCN is a collaboration among 26 research collections, and includes vertebrate and invertebrate taxonomists and curators, epidemiologists, ecologists, data-scientists, and biodiversity informatics specialists. This Partners to Existing Networks (PEN) grant allows the Yale Peabody Museum to join the collaboration, and digitize specimens that fill critical gaps in geographic and taxonomic coverage in the existing TPT-TCN. This project will integrate arthropod data with millions of vertebrate host records with vector and disease monitoring data shared by state and federal agency collaborators, creating a novel foundation for integrative, long-term research. It will also empower ongoing citizen science and public awareness campaigns with tools for understanding distribution changes of arthropod vectors and associated diseases due to environmental change and global movement. Educational initiatives include partnering with natural history museums to educate the public about parasites via science-focused lectures, exhibits, summer youth programs, informal presentations, and developing new online educational resources for teachers in underserved communities. All specimen images generated by this project will be shared with iDigBio.org and used in developing a rapid parasite identification tool, which will be accessible over the internet and smartphone apps. The TPT-TCN will also develop and implement undergraduate teaching modules focused on data held in natural history collections. These modules will be disseminated to academic institutions across the United States and made available online.

Project Sponsor: Yale University (NSF Award #2001547)

Principal Investigators: Lawrence Gall (PI), Stephen Cameron (co-PI)

2021 Adding a world-class flea collection to the Terrestrial Parasite Tracker Network

Parasitic insects have a global impact on human health, livestock production, and wildlife conservation. Building robust datasets of parasites’ host preferences, seasonal activity, and geographic range can help scientists and public health professionals understand and predict patterns of disease transmission; however, much of the data needed for these assessments is accessible only through museum collections. The primary goal of this project is to extract this data from a world-class collection of fleas and associated parasites at the Carnegie Museum of Natural History (CMNH). As part of the Terrestrial Parasite Tracker Thematic Collections Network (TPT TCN), high-quality specimen images and host/locality data will be captured, digitized, and shared via public data portals. This will allow entomologists, epidemiologists, and other researchers to make essential connections between disease vectors and their host species. In turn, understanding these connections will support future assessments of economic and health risks from insect-vectored disease.

The Robert Traub flea collection at CMNH is one of the largest and most meticulously curated collections of mammal parasites in the world, with 74,897 specimens mounted under glass on 60,596 glass slides with 4,615 associated genitalic dissections. This project will use automated slide scanning technology developed for pathology laboratory use to capture whole-slide and specimen images efficiently. These images will then be linked with digitized host and locality data from both slide labels and Traub’s fieldwork logs. This project will more than quintuple the Siphonaptera specimen records for the Terrestrial Parasite Tracker TCN and complete its representation of flea families. This will represent a valuable dataset and image resource not just for TPT TCN and epidemiology research, but for systematic research on Siphonaptera in general. Disseminating this data through the online data portals, including iDigBio.org, Symbiota Collection of Arthropods Network (SCAN), and the Global Biodiversity Information Facility (GBIF). Broad digital access will enable researchers and diagnosticians worldwide to access an enormous database of host-parasite relationships as well as to compare their specimens to high-quality specimen images with reliable species-level identifications.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Project Sponsor: Carnegie Institute (NSF Award #2101926)

Principal Investigators: Ainsley Seago (PI)